The sequence analysis of cDNA clones have shown: a) Rat alpha-LA is larger than any known alpha-lactalbumins. It has 17 extra residues beyond the COOH terminus of the alpha-lactalbumin isolated and sequenced to date from other species. The predicted COOH-terminal sequence is hydrophobic and proline rich and bears some resemblance to beta-casein sequences; b) Rat whey phosphoproteins contain high content of cysteine, glutamic acid, aspartic acid and serine, but lack tyrosine. The cysteines appear in unique arrangements and are repeated in two domains of the protein. The second domain has striking similarities with the second domain of the red sea turtle protease inhibitor; c) The encloded k-protein sequence lacks in cysteine and has several potential phosphorylation sites. Methylation of alpha-LA, whey phosphoprotein and k-protein gene sequences in the rat mammary gland at various stages of functional differentiation and several rat mammary tumors have shown an inverse relationship between the expression of alpha-LA, Wp or k- gene and the methylation of this gene sequences.